Table 4.
GO Categories Enriched for Positively Selected Genes, Based on Scores from the Branch-Site Test from Codeml in Drosophila.
| SetID | Ontology | SetName | SetSize | Score | P-value | FDR |
|---|---|---|---|---|---|---|
| GO:0006030 | BP | Chitin metabolic process | 29 | 16.2 | 4.0e-6 | 0.0015 |
| GO:0006022 | BP | Aminoglycan metabolic process | 36 | 19.4 | 5.7e-6 | 0.0018 |
| GO:0006952 | BP | Defense response | 36 | 19.2 | 9.8e-6 | 0.0018 |
| GO:0008061 | MF | Chitin binding | 24 | 13.5 | 2.0e-5 | 0.0020 |
| GO:0004252 | MF | Serine-type endopeptidase activity | 52 | 26.0 | 3.3e-5 | 0.0023 |
| GO:0008026 | MF | ATP-dependent helicase activity | 18 | 10.5 | 4.0e-5 | 0.0026 |
| GO:0004872 | MF | Receptor activity | 13 | 7.9 | 8.5e-5 | 0.0048 |
| GO:0006006 | BP | Glucose metabolic process | 13 | 7.8 | 0.00021 | 0.0082 |
| GO:0046486 | BP | Glycerolipid metabolic process | 17 | 9.7 | 0.00023 | 0.0090 |
| GO:0005819 | CC | Spindle | 20 | 10.9 | 0.00046 | 0.012 |
| GO:0004175 | MF | Endopeptidase activity | 78 | 35.9 | 0.00048 | 0.012 |
| GO:0009607 | BP | Response to biotic stimulus | 31 | 15.8 | 0.00060 | 0.013 |
| GO:0051707 | BP | Response to other organism | 31 | 15.8 | 0.00060 | 0.013 |
| GO:0006508 | BP | Proteolysis | 136 | 59.5 | 0.00071 | 0.014 |
| GO:0006007 | BP | Glucose catabolic process | 12 | 7.0 | 0.00072 | 0.014 |
| GO:0019320 | BP | Hexose catabolic process | 12 | 7.0 | 0.00072 | 0.014 |
| GO:0030312 | CC | External encapsulating structure | 12 | 7.0 | 0.00074 | 0.014 |
| GO:0015081 | MF | Sodium ion transmembrane transporter activity | 16 | 8.9 | 0.00088 | 0.016 |
| GO:0051649 | BP | Establishment of localization in cell | 14 | 7.9 | 0.00093 | 0.017 |
| GO:0007126 | BP | Meiosis | 34 | 16.9 | 0.00096 | 0.017 |
| GO:0003824 | MF | Catalytic activity | 844 | 337.0 | 0.0011 | 0.018 |
| GO:0046488 | BP | Phosphatidylinositol metabolic process | 11 | 6.5 | 0.0012 | 0.018 |
| GO:0016490 | MF | Structural constituent of peritrophic membrane | 11 | 6.4 | 0.0013 | 0.018 |
| GO:0005975 | BP | Carbohydrate metabolic process | 64 | 29.5 | 0.0015 | 0.019 |
| GO:0004888 | MF | Transmembrane receptor activity | 49 | 23.2 | 0.0016 | 0.020 |
| GO:0051276 | BP | Chromosome organization | 59 | 27.2 | 0.0020 | 0.024 |
| GO:0008270 | MF | Zinc ion binding | 173 | 73.4 | 0.0027 | 0.029 |
| GO:0002376 | BP | Immune system process | 43 | 20.4 | 0.0027 | 0.029 |
| GO:0002759 | BP | Regulation of antimicrobial humoral response | 11 | 6.3 | 0.0028 | 0.029 |
| GO:0004984 | MF | Olfactory receptor activity | 19 | 9.9 | 0.0030 | 0.029 |
| GO:0002697 | BP | Regulation of immune effector process | 11 | 6.2 | 0.0038 | 0.035 |
| GO:0000819 | BP | Sister chromatid segregation | 11 | 6.2 | 0.0038 | 0.035 |
| GO:0007143 | BP | Female meiosis | 11 | 6.2 | 0.0047 | 0.040 |
| GO:0016021 | CC | Integral to membrane | 224 | 93.1 | 0.0047 | 0.040 |
| GO:0031347 | BP | Regulation of defense response | 12 | 6.6 | 0.0055 | 0.044 |
| GO:0015370 | MF | Solute:sodium symporter activity | 12 | 6.6 | 0.0061 | 0.047 |
| GO:0000272 | BP | Polysaccharide catabolic process | 11 | 6.1 | 0.0065 | 0.049 |
| GO:0016810 | MF | Hydrolase activity, acting on carbon–nitrogen (but not peptide) bonds | 28 | 13.6 | 0.0065 | 0.049 |
| GO:0004521 | MF | Endoribonuclease activity | 11 | 6.1 | 0.0069 | 0.052 |
| GO:0007291 | BP | Sperm individualization | 14 | 7.4 | 0.0074 | 0.053 |
| GO:0010564 | BP | Regulation of cell cycle process | 30 | 14.4 | 0.0075 | 0.053 |
| GO:0005635 | CC | Nuclear envelope | 17 | 8.7 | 0.0077 | 0.054 |
| GO:0016773 | MF | Phosphotransferase activity, alcohol group as acceptor | 82 | 36.0 | 0.0077 | 0.054 |
| GO:0051253 | BP | Negative regulation of RNA metabolic process | 35 | 16.5 | 0.0080 | 0.055 |
| GO:0007608 | BP | Sensory perception of smell | 21 | 10.5 | 0.0080 | 0.055 |
| GO:0004222 | MF | Metalloendopeptidase activity | 26 | 12.7 | 0.0082 | 0.055 |
| GO:0006807 | BP | Nitrogen compound metabolic process | 298 | 121.5 | 0.0090 | 0.059 |
| GO:0005576 | CC | Extracellular region | 97 | 41.9 | 0.010 | 0.066 |
| GO:0006814 | BP | Sodium ion transport | 19 | 9.5 | 0.011 | 0.068 |
| GO:0045132 | BP | Meiotic chromosome segregation | 11 | 5.9 | 0.011 | 0.070 |
| GO:0034641 | BP | Cellular nitrogen compound metabolic process | 296 | 120.4 | 0.012 | 0.072 |
| GO:0010629 | BP | Negative regulation of gene expression | 42 | 19.2 | 0.013 | 0.073 |
| GO:0090304 | BP | Nucleic acid metabolic process | 162 | 67.6 | 0.013 | 0.075 |
| GO:0016301 | MF | Kinase activity | 91 | 39.2 | 0.013 | 0.075 |
| GO:0048584 | BP | Positive regulation of response to stimulus | 11 | 5.9 | 0.015 | 0.084 |
| GO:0016798 | MF | Hydrolase activity, acting on glycosyl bonds | 26 | 12.4 | 0.017 | 0.086 |
| GO:0006139 | BP | Nucleobase, nucleoside, nucleotide, and nucleic acid metabolic process | 236 | 96.4 | 0.017 | 0.086 |
| GO:0016491 | MF | Oxidoreductase activity | 201 | 82.6 | 0.018 | 0.090 |
| GO:0009987 | BP | Cellular process | 790 | 310.5 | 0.019 | 0.095 |
| GO:0007088 | BP | Regulation of mitosis | 16 | 8.0 | 0.019 | 0.095 |
| GO:0051783 | BP | Regulation of nuclear division | 16 | 8.0 | 0.019 | 0.095 |
| GO:0006810 | BP | Transport | 200 | 82.1 | 0.021 | 0.10 |
| GO:0051234 | BP | Establishment of localization | 197 | 80.9 | 0.021 | 0.10 |
| GO:0006066 | BP | Alcohol metabolic process | 35 | 16.1 | 0.021 | 0.10 |
| GO:0004553 | MF | Hydrolase activity, hydrolyzing O-glycosyl compounds | 22 | 10.6 | 0.022 | 0.11 |
| GO:0008233 | MF | Peptidase activity | 26 | 12.3 | 0.022 | 0.11 |
| GO:0070011 | MF | Peptidase activity, acting on l-amino acid peptides | 22 | 10.6 | 0.022 | 0.11 |
| GO:0046914 | MF | Transition metal ion binding | 58 | 25.5 | 0.022 | 0.11 |
| GO:0050660 | MF | Flavin adenine dinucleotide binding | 16 | 8.0 | 0.024 | 0.11 |
| GO:0045892 | BP | Negative regulation of transcription, DNA-dependent | 26 | 12.2 | 0.024 | 0.11 |
| GO:0032553 | MF | Ribonucleotide binding | 161 | 66.5 | 0.024 | 0.11 |
| GO:0032555 | MF | Purine ribonucleotide binding | 161 | 66.5 | 0.024 | 0.11 |
| GO:0035639 | MF | Purine ribonucleoside triphosphate binding | 161 | 66.5 | 0.024 | 0.11 |
| GO:0006396 | BP | RNA processing | 36 | 16.4 | 0.025 | 0.11 |
| GO:0031226 | CC | Intrinsic to plasma membrane | 30 | 13.9 | 0.026 | 0.11 |
| GO:0035222 | BP | Wing disc pattern formation | 11 | 5.7 | 0.026 | 0.12 |
| GO:0007346 | BP | Regulation of mitotic cell cycle | 31 | 14.3 | 0.028 | 0.12 |
| GO:0045017 | BP | Glycerolipid biosynthetic process | 11 | 5.7 | 0.030 | 0.13 |
| GO:0006955 | BP | Immune response | 30 | 13.8 | 0.030 | 0.13 |
| GO:0044262 | BP | Cellular carbohydrate metabolic process | 44 | 19.6 | 0.030 | 0.13 |
| GO:0017076 | MF | Purine nucleotide binding | 164 | 67.5 | 0.032 | 0.14 |
| GO:0016705 | MF | Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 21 | 10.0 | 0.032 | 0.14 |
| GO:0005524 | MF | ATP binding | 163 | 67.0 | 0.034 | 0.14 |
| GO:0030554 | MF | Adenyl nucleotide binding | 163 | 67.0 | 0.034 | 0.14 |
| GO:0032559 | MF | Adenyl ribonucleotide binding | 163 | 67.0 | 0.034 | 0.14 |
| GO:0008237 | MF | Metallopeptidase activity | 12 | 6.1 | 0.034 | 0.14 |
| GO:0007127 | BP | Meiosis I | 18 | 8.7 | 0.035 | 0.14 |
| GO:0019730 | BP | Antimicrobial humoral response | 14 | 6.9 | 0.039 | 0.15 |
| GO:0005815 | CC | Microtubule organizing center | 16 | 7.8 | 0.041 | 0.16 |
| GO:0055114 | BP | Oxidation–reduction process | 167 | 68.3 | 0.043 | 0.17 |
| GO:0019899 | MF | Enzyme binding | 14 | 6.9 | 0.044 | 0.17 |
| GO:0048232 | BP | Male gamete generation | 45 | 19.8 | 0.045 | 0.17 |
| GO:0008033 | BP | tRNA processing | 17 | 8.2 | 0.045 | 0.17 |
| GO:0005887 | CC | Integral to plasma membrane | 29 | 13.2 | 0.046 | 0.17 |
| GO:0044281 | BP | Small molecule metabolic process | 212 | 85.8 | 0.046 | 0.17 |
| GO:0008238 | MF | Exopeptidase activity | 18 | 8.6 | 0.046 | 0.17 |
| GO:0051179 | BP | Localization | 236 | 95.1 | 0.047 | 0.17 |
| GO:0007283 | BP | Spermatogenesis | 44 | 19.3 | 0.047 | 0.18 |
| GO:0050662 | MF | Coenzyme binding | 48 | 21.0 | 0.048 | 0.18 |
| GO:0034470 | BP | ncRNA processing | 27 | 12.3 | 0.049 | 0.18 |
| GO:0048515 | BP | Spermatid differentiation | 24 | 11.1 | 0.050 | 0.18 |
| GO:0045786 | BP | Negative regulation of cell cycle | 11 | 5.5 | 0.050 | 0.18 |
| GO:0045934 | BP | Negative regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolic process | 41 | 18.1 | 0.052 | 0.18 |
| GO:0010639 | BP | Negative regulation of organelle organization | 12 | 5.9 | 0.055 | 0.19 |
| GO:0015631 | MF | Tubulin binding | 12 | 5.9 | 0.056 | 0.19 |
| GO:0005549 | MF | Odorant binding | 43 | 18.8 | 0.058 | 0.20 |
Note.—Depletion results are shown in supplementary table S4, Supplementary Material online.